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| 1 | Genome-level diversification of eight ancient tea populations in the Guizhou and Yunnan regions identifies candidate genes for core agronomic traits显示文摘The ancient tea plant,as a precious natural resource and source of tea plant genetic diversity,is of great value for studying the evolutionary mechanism,diversification,and domestication of plants.The overall genetic diversity among ancient tea plants and the genetic changes that occurred during natural selection remain poorly understood.Here,we report the genome resequencing of eight different groups consisting of 120 ancient tea plants:six groups from Guizhou Province and two groups from Yunnan Province.Based on the 8,082,370 identified high-quality SNPs,we constructed phylogenetic relationships,assessed population structure,and performed genome-wide association studies(GWAS).Our phylogenetic analysis showed that the 120 ancient tea plants were mainly clustered into three groups and five single branches,which is consistent with the results of principal component analysis(PCA).Ancient tea plants were further divided into seven subpopulations based on genetic structure analysis.Moreover,it was found that the variation in ancient tea plants was not reduced by pressure from the external natural environment or artificial breeding(nonsynonymous/synonymous=1.05).By integrating GWAS,selection signals,and gene function prediction,four candidate genes were significantly associated with three leaf traits,and two candidate genes were significantly associated with plant type.These candidate genes can be used for further functional characterization and genetic improvement of tea plants. | Litang Lu Hufang Chen Xiaojing Wang Yichen Zhao Xinzhuan Yao Biao Xiong Yanli Deng Degang Zhao | 2021 | Horticulture Research2021，8，1： | 3 |
| 2 | SARS-CoV-2 impairs the disassembly of stress granules and promotes ALS-associated amyloid aggregation显示文摘The nucleocapsid(N)protein of SARS-CoV-2 has been reported to have a high ability of liquid-liquid phase separation,which enables its incorporation into stress granules(SGs)of host cells.However,whether SG invasion by N protein occurs in the scenario of SARS-CoV-2 infection is unknow,neither do we know its con-sequence.Here,we used SARS-CoV-2 to infect mam-malian cells and observed the incorporation of N protein into SGs,which resulted in markedly impaired self-dis-assembly but stimulated cell cellular clearance of SGs.NMR experiments further showed that N protein binds to the SG-related amyloid proteins via non-specific tran-sient interactions,which not only expedites the phase transition of these proteins to aberrant amyloid aggre-gation in vitro,but also promotes the aggregation of FUS with ALS-associated P525L mutation in cells.In addition,we found that ACE2 is not necessary for the infection of SARS-CoV-2 to mammalian cells.Our work indicates that SARS-CoV-2 infection can impair the dis-assembly of host SGs and promote the aggregation of SG-related amyloid proteins,which may lead to an increased risk of neurodegeneration. | Yichen Li Shuaiyao Lu Jinge Gu Wencheng Xia Shengnan Zhang Shenqing Zhang Yan Wang Chong Zhang Yunpeng Sun Jian Lei Cong Liu Zhaoming Su Juntao Yang Xiaozhong Peng Dan Li | 2022 | Protein & Cell2022，13，8： | 1 |
| 3 | Maternal genetic history of ancient Tibetans over the past 4000 years显示文摘The settlement of the Tibetan Plateau epitomizes human adaptation to a high-altitude environment that poses great challenges to human activity.Here,we reconstruct a 4000-year maternal genetic history of Tibetans using 128 ancient mitochondrial genome data from 37 sites in Tibet.The phylogeny of haplotypes M9a1a,M9a1b,D4g2,G2a’c,and D4i show that ancient Tibetans share the most recent common ancestor with ancient Middle and Upper Yellow River populations around the Early and Middle Holocene.In addition,the connections between Tibetans and Northeastern Asians vary over the past 4000 years,with a stronger matrilineal connection between the two during 4000 BPe3000 BP,and a weakened connection after 3000 BP,that are coincident with climate change,followed by a reinforced connection after the Tubo period(1400 BPe1100 BP).Besides,an over 4000-year matrilineal continuity is observed in some of the maternal lineages.We also find the maternal genetic structure of ancient Tibetans is correlated to the geography and interactions between ancient Tibetans and ancient Nepal and Pakistan populations.Overall,the maternal genetic history of Tibetans can be characterized as a long-term matrilineal continuity with frequent internal and external population interactions that are dynamically shaped by geography,climate changes,as well as historical events. | Ganyu Zhang Can Cui Shargan Wangdue Hongliang Lu Honghai Chen Lin Xi Wei He Haibing Yuan Tinley Tsring Zujun Chen Feng Yang Tashi Tsering Shuai Li Norbu Tashi Tsho Yang Yan Tong Xiaohong Wu Linhui Li Yuanhong He Peng Cao Qingyan Dai Feng Liu Xiaotian Feng Tianyi Wang Ruowei Yang Wanjing Ping Ming Zhang Xing Gao Yichen Liu Wenjun Wang Qiaomei Fu | 2023 | Journal of Genetics and Genomics2023，50，10： | 1 |
| 4 | A Method of layer-by-layer gold nanoparticle hybridization in a quartz crystal microbalance DNA sensing system used to detect dengue virus显示文摘 | Chen SH Chuang Yaochen Lu Yichen | 2009 | Nanotechnology2009，20，： | 1 |
| 5 | Population Structure Analysis and Genome-Wide Association Study of Tea(Camellia sinensis(L.)Kuntze)Germplasm in Qiannan,China,Based on SLAF-Seq Technology显示文摘Duyun Maojian tea is a famous tea in China.In this study,the specific-locus amplified fragment(SLAF)sequencing method was used to analyze the population structure and conduct a genome-wide association study(GWAS)of 2 leaf traits of 123 tea plants in Qiannan,China.A total of 462,019 SLAF tags and 11,362,041 single-nucleotide polymorphism(SNP)loci were obtained.The results of phylogenetic tree analysis,cluster analysis,and principal component analysis showed that 123 tea germplasms were clustered into three groups,and the heterozygosity rates for Groups I,II,and II were 0.206,0.224,and 0.34,respectively.Generally,tea germplasms in a production area are clustered in a group,indicating that tea germplasms in different production areas have certain genetic diversity.The traditional Duyun Maojian tea core production areas,TS and DC-SJ,are clustered into Group I and Group II respectively,while the ZY production area is relatively independent in Group III.Furthermore,based on GWAS analysis,11 candidate genes related to leaf apex and 7 candidate genes related to leaf shape were obtained.This study clarified the genetic relationship among eight Duyun Maojian tea production areas and obtained candidate genes related to leaf apex and leaf shape development.The results showed that population structure and candidate genes are an effective basis for the breeding of Duyun Maojian tea germplasm. | Fen Zhang Weili Tian Lu Cen Litang Lv Xiaofang Zeng Yulu Chen Yichen Zhao Yan Li | 2022 | Phyton-International Journal of Experimental Botany2022，91，4： | 1 |
| 6 | A comprehensive evaluation of flowering plant diversity and conservation priority for national park planning in China显示文摘Establishment of a national park protection system in China,including the latest target proposed to protect at least 30%of the land area,calls for a comprehensive exploration of conservation priorities incorporating multiple diversity facets.We herein evaluate the spatial distribution of Chinese flowering plants from the perspectives of richness,uniqueness,vulnerability,and evolutionary history,by integrating three mega-phylogenies and comprehensive distribution data.We detect significantly high consistency among hotspots of different diversity measures for Chinese flowering plants,suggesting that multiple facets of evolutionary diversity are concentrically distributed in China.Affording legal protection to these areas is expected to maximize positive conservation outcomes.We propose two integrative diversity indices by incorporating three richness-based and three phylogeny-based measures,respectively.Both methods identify areas with high species richness,but the integrative phylogeny-based index also locates key areas with ancient and unique evolutionary histories(e.g.,Ailao-Wuliang Mts,Dabie Mts,Hainan rainforest,Karst area of Yunnan-Guizhou-Guangxi,Nanling Mts,and southeast coastal regions).Of all the diversity indices explored,phylogenetic endemism maximizes the incidental protection of other indices in most cases,emphasizing its significance for conservation planning.Finally,42 priority areas are identified by combining the 5%-criterion hotspots of two integrative indices and the minimum area to protect all threatened species analyzed.These priorities cover only 13.3%of China's land area,but host 97.1%of species richness(23,394/24,095),96.5%of endemic species(11,841/12,274),100%of threatened species(2,613/2,613),and 99.3%of phylogenetic diversity for flowering plants involved in this study.These frameworks provide a solid scientific basis for national park planning in China. | Limin Lu Lina Zhao Haihua Hu Bing Liu Yuchang Yang Yichen You Danxiao Peng Russell L.Barrett Zhiduan Chen | 2023 | Fundamental Research2023，3，6： | 1 |
| 7 | Constrained planar motion analysis by decomposition 显示文摘 | Long Quan Yichen Wei Le Lu | 2004 | Image and Vision Computing2004，22，： | 1 |
| 8 | Energy consumption and economic growth in China: A multivariate causality test显示文摘 | Yuan Wang Yichen Wang Jing Zhou Xiaodong Zhu Genfa Lu | 2011 | Energy Policy2011，，39： | 1 |
| 9 | Mean square exponential stability and periodic solutions of stochastic delay cellular neural net- works 显示文摘 | LU Junxiang MA Yichen | 2008 | Chaos Solutions and Fractals2008，38，： | 1 |
| 10 | Infectious Simian/Human Immunodeficiency Virus with Human Immunodeficiency virus Type 1 subtype C from an African isolate: Rhesus Macaque Model显示文摘 | Thumbi Ndung'u Yichen Lu Boris Renjifo | 2001 | J Virol2001，75，11： | 1 |
| 11 | TNFR2 is a potent prognostic biomarker for post-transplant lung metastasis in patients with hepatocellular carcinoma显示文摘Objective:Lung metastasis is a common and fatal complication of liver transplantation for hepatocellular carcinoma(HCC).The precise prediction of post-transplant lung metastasis in the early phase is of great value.Methods:The mRNA profiles of primary and paired lung metastatic lesions were analyzed to determine key signaling pathways.We enrolled 241 HCC patients who underwent liver transplantation from three centers.Tissue microarrays were used to evaluate the prognostic capacity of tumor necrosis factor(TNF),tumor necrosis factor receptor 1(TNFR1),and TNFR2,particularly for post-transplant lung metastasis.Results:Comparison of primary and lung metastatic lesions revealed that the TNF-dependent signaling pathway was related to lung metastasis of HCC.The expression of TNF was degraded in comparison to that in para-tumor tissues(P<0.001).The expression of key receptors in the TNF-dependent signaling pathway,TNFR1 and TNFR2,was higher in HCC tissues than in para-tumor tissues(P<0.001).TNF and TNFR1 showed no relationship with patients’outcomes,whereas elevated TNFR2 in tumor tissue was significantly associated with worse overall survival(OS)and increased recurrence risk(5-year OS rate:31.9%vs.62.5%,P<0.001).Notably,elevated TNFR2 levels were also associated with an increased risk of post-transplant lung metastasis(hazard ratio:1.146;P<0.001).Cox regression analysis revealed that TNFR2,Hangzhou criteria,age,and hepatitis B surface antigen were independent risk factors for post-transplant lung metastasis,and a novel nomogram was established accordingly.The nomogram achieved excellent prognostic efficiency(area under time-dependent receiver operating characteristic=0.755,concordance-index=0.779)and was superior to conventional models,such as the Milan criteria.Conclusions:TNFR2 is a potent prognostic biomarker for predicting post-transplant lung metastasis in patients with HCC.A nomogram incorporating TNFR2 deserves to be a helpful prognostic tool in liver transplantation for HCC. | Huigang Li Zuyuan Lin Jianyong Zhuo Modan Yang Wei Shen Zhihang Hu Yichen Ding Hao Chen Chiyu He Xinyu Yang Siyi Dong Xuyong Wei Beicheng Sun Shusen Zheng Ren Lang Di Lu Xiao Xu | 2023 | Chinese Journal of Cancer Research2023，35，1： | 0 |
| 12 | DNA methylation mediated by RdDM pathway and demethylation affects furanone accumulation through regulation of QUINONE OXIDOREDUCTASE in strawberry显示文摘Recently,increasing evidence suggests that DNA methylation plays a crucial role in fruit ripening.However,the role of DNA methylation in regulating specific traits,such as flavor,remains unclear.Here,we report a role of DNA methylation in affecting furanone biosynthesis in strawberry.Strawberry quinone oxidoreductase(FaQR)is a key enzyme in furanone biosynthesis.There are four FaQR homologs in strawberry cultivar‘Yuexin’,and one of them,FaQR3,contributes∼50%of FaQR transcripts,indicating a major role of FaQR3 in furanone biosynthesis.Through characterization of levels of DNA methylation and FaQR3 transcript and furanone contents during fruit ripening and after the application of DNA methylation inhibitor,we found that the DNA methylation level of the FaQR3 promoter was negatively correlated with FaQR3 expression and furanone accumulation,suggesting that DNA methylation may be involved in furanone biosynthesis through adjusting FaQR3 expression,and responded to different temperatures consistently.In addition,transient expression of a gene in the RNA-directed DNA methylation(RdDM)pathway,FaAGO4,and enrichment analysis of the 24-nucleotide siRNAs suggested that DNA methylation in the FaQR3 promoter is mediated by the RdDM pathway.Transient RNA interference(RNAi)of FaDML indicated that the demethylation pathway may be involved in regulating furanone accumulation.These findings provide new insights into the role of DNA methylation and demethylation in affecting flavor quality in strawberry during fruit ripening. | Yunduan Li Yanna Shi Yichen Li Jiao Lu Yunfan Sun Yuanyuan Zhang Wenbo Chen Xiaofang Yang Donald Grierson Zhaobo Lang Guihua Jiang Kunsong Chen | 2023 | Horticulture Research2023，10，8： | 0 |
| 13 | Micro Hierarchical Structure and Mechanical Property of Sparrow Hawk (Accipiter nisus) Feather Shaf显示文摘In this study,the real 3D model of the feather shaft that is composed of medulla and cortex is characterized by X-ray computer tomography,and the structural features are quantitatively analyzed.Compression and tensile tests are conducted to evaluate the mechanical performance of the feather shaft and cortex at different regions.The analysis of the 3D model shows that the medulla accounts for∼70%of the shaft volume and exhibits a closed-cell foam-like structure,with a porosity of 59%.The cells in the medulla show dodecahedron and decahedron morphology and have an equivalent diameter of∼30μm.In axial compression,the presence of medulla enhances the shaft stability.Especially,the combined effect of the medulla and cortex increases the buckling strength of the middle and distal shaft by 77%and 141%,respectively,compared to the calculated value of the shaft using linear mixed rule.The tensile properties of the cortex along the shaft axis are anisotropic because of the different fiber structures.As the fiber orientation gradually becomes uniform in the axial direction,the Young’s modulus and tensile strength of the cortex on the dorsal gradually increase from calamus to the distal shaft,and the fracture mode changes from tortuous fracture to V-shaped fracture.The cortex on the lateral shows the opposite trend,that is the distal shaft becomes weaker due to fiber tangles. | Yichen Lu Zongning Chen Enyu Guo Xiangqing Kong Huijun Kang Yanjin Xu Rengeng Li Guohua Fan Tongmin Wang | 2021 | Computer Modeling in Engineering & Sciences2021，，5： | 0 |
| 14 | Role of Intraseasonal Oscillation in a Compound Drought and Heat Event over the Middle of the Yangtze River Basin during Midsummer 2018显示文摘In late July 2018, a compound drought and heat event(CDHE) occurred in the middle of the Yangtze River basin(MYRB) and caused great damage to the national economy. The CDHE over the MYRB has been documented to be linked with intraseasonal oscillations(ISOs) from different regions. However, specific roles of different ISOs on the development of the CDHE cannot be separated in the observational analysis. By using partial lateral forcing experiments driven by ISO in the Weather Research and Forecasting(WRF) model, we found that the midlatitude ISO generated by a westerly wave train in the upper troposphere played an important role in this heatwave and drought event in the northern MYRB, causing a regional average temperature rise of 1.65°C and intensification of drought over23.49% of the MYRB area. On the other hand, the ISO associated with the Pacific-Japan(PJ)-like teleconnection wave train in the lower troposphere induced a more pronounced impact on the event, causing an average temperature rise of 2.44°C, intensifying drought over 29.62% of the MYRB area. The MYRB was mainly affected by northward warm advection driven by the westward extension of the western North Pacific subtropical high in the early period of the CDHE development. In the late period, because of the establishment of a deep positive geopotential height field through the troposphere leading to intensive local subsidence, there was a remarkable temperature rise and moisture decrease in the MYRB. The results will facilitate a better understanding of the occurrence of CDHE and provide empirical precursory signals for subseasonal forecast of CDHE. | Chuhan LU Yichen SHEN Yonghua LI Bo XIANG Yujing QIN | 2022 | Journal of Meteorological Research2022，36，4： | 0 |
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